tbuckley/cabot-search huggingface dataset:
Abstract 1488: The FOXA2 contributes to tumor proliferation and invasion via HGF mediated ERK signaling pathway in human gastric cancer
Authors: Jiyoon Jung, Sungae Koh, Kyunghee Lee
Journal: Cancer Research (2023)

Abstract Background: FOXA1 and FOXA2, members of the forkhead transcription factor family, are critical for epithelial differentiation in many endoderm-derived organs and important regulators in body homeostasis. It has been shown that FOXA2 plays an important role in tumorigenesis and carcinogenesis in glioma, breast cancer, hepatoma, and others. However, FOXA2 has not yet been elucidated on the tumorigenesis, proliferation, and invasion of human gastric cancer, and needs to be researched and discovered. In this study, the HGF-mediated association of FOXA2, extracellular signal-regulated protein kinase (ERK), and matrix metalloproteinase 9 (MMP9) and cancer cell proliferation and invasion were investigated in two types of human gastric cancer cell lines. Methods: In this study, cell culture, cDNA microarray analysis, western blotting, Real-time Polymerase chain reaction, Zymography, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay, FOXA2 knock-down with short hairpin RNA (shRNA), chromatin immunoprecipitation assay, Standard two chamber invasion assay. Results: First, we confirmed that the expression level of FOXA2 was up-regulated by HGF (hepatocyte growth factor) in human gastric cancer cells. To identify the associated pathway of HGF-induced FOXA2 about ERK, MMP9 expression, the cells were treated with PI3K (Phosphoinositide 3-kinase) inhibitor (LY294002) and then analyzed by Western blotting. The role of FOXA2 associated with MMP9 and ERK was determined by knockdown cell of FOXA2. FOXA2-sh RNA cells showed a decreased level of MMP9 and ERK. HGF-mediated cell proliferation and invasion were decreased in FOXA2 knockdown cell. Conclusions: These results suggest that FOXA2 plays an important role in cell proliferation and metastasis in hepatocellular carcinoma, and FOXA2 may be a novel target for the prevention of progression and treatment of human gastric cancer. Citation Format: Jiyoon Jung, Sungae Koh, Kyunghee Lee. The FOXA2 contributes to tumor proliferation and invasion via HGF mediated ERK signaling pathway in human gastric cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1488.
Abstract 6596: Genomic and proteome analysis using preoperative cell free DNA and extracellular vesicles of lung cancer patients
Authors: Hayato Koba, Hideharu Kimura, Seiji Yano
Journal: Cancer Research (2023)

Abstract Background: The detection of circulating cell free DNA (cfDNA) has been examined as a predictor of postoperative recurrence and survival in lung cancer patients. Extracellular vesicles (EVs) have potent for searching a new target to cancers. Objective: To analyze the association between cfDNA/EVs and prognosis after lung cancer surgery. Methods: We retrospectively examined patient background, disease-free survival, overall survival, and preoperative cfDNA in lung cancer patients who underwent surgery at Kanazawa University Hospital between January 2017 and May 2020, in whom preoperative chemotherapy was not administered. We extracted cfDNA from 4 ml plasma within 7 days before surgery and measured its concentration. EVs were extracted from 500 μl serum via Tim4 protein. Proteins included in EVs were analyzed by mass spectrometry. Results: 285 patients were included, 179 males and 106 females, median age 71(36-88) years, and 8 patients had SCLC. EGFRm- positive lung cancer was included in 93 cases (32.6%). The pStage0/l/ll/lll/lV of NSCLC was 7/187/42/36/6 respectively, and the pStagel/ll/lll of SCLC was 4/1/3 respectively. The mDFS of NSCLC was 14.6 (7.8-29.7)/21.5 (8.5-NA) months in pStage lll/lV, respectively. mOS was 53.3 (28.7-NA) months in pStage lll and was not achieved in other stages. The mDFS of SCLC was 19.8 (1.9-NA)/NA/5.7 (1.9-NA) months in pStage l/ll/lll, respectively. mOS was NA/NA/9.3 (9.3-NA) months, respectively. cfDNA was detected in 283 (99.2%) patients, with a concentration of 4.7 (0-60.0) ng/μl. The correlation coefficient between cfDNA concentration and DFS/OS in NSCLC was -0.023 (P=0.70)/-0.014 (P=0.81). The correlation coefficient between cfDNA concentration and DFS/OS for SCLC was -0.86 (P=0.024)/-0.89 (P=0.012). No recurrence was observed in patients in whom cfDNA was not detected.EVs were detectable from pre-operative serum samples, and the proteins included in these were different, whether disease was recurrent or not. Conclusion: The cfDNA concentration did not correlate with DFS/OS in post-operative NSCLC, whereas it correlated negatively with DFS/OS in SCLC. In the presentation, we will further discuss about the concrete genetic alterations and protein expression, based on the cfDNA sequencing and proteomics analysis. Citation Format: Hayato Koba, Hideharu Kimura, Seiji Yano. Genomic and proteome analysis using preoperative cell free DNA and extracellular vesicles of lung cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6596.
Abstract 2565: Divergentnucleocytoplasmic transport influences escape from HER2-activated DCIS-like state
Authors: Lixin Wang, Bishal Paudel, Anthony McKnight, Kevin Janes
Journal: Cancer Research (2023)

Abstract HER2/ErbB2 and EGFR/ErbB1 activation incite a phenotype resembling premalignant escape from ductal carcinoma in situ (DCIS) in the 3D multicellular arrangement of breast-epithelial cells. This phenomenon tends to be infrequent, and the exact mechanism for its heterogeneous presentation has been elusive. We sought to investigate the process by which ErbB receptors facilitate a picture of incomplete penetrance in DCIS escape (DE). To identify the transcriptional signatures that prime cells towards DE, we randomly profiled 10-cell transcriptomes of single spheroids after 24 hours of ERBB activation, and frequency matched gene expression to the DE-phenotype. We uncovered a network of nucleocytoplasmic transport (NCT) regulators that alter the DE-phenotype penetrance. Of the regulators, CSE1L (an exportin) synergistically increases the DE-frequency when induced, while its knockdown reduces the phenotype, suggesting its functional role. Furthermore, we evaluated the significance of this result in vivo by perturbing Cse1l in Erbb2-amplified mouse mammary-gland tumors and found that activation of Erbb2 (mimicked by ERBB-inhibitor release) alters the macroscale organization of tumors, reminiscent of DE. Specifically, we found an elevated CSE1L inhibits an accumulation of classical nuclear-localizing cargoes that require binding with importin-α/β (KPNAs, KPNB1) complexes. Using proximity labeling with BirA*-fused with CSE1L, we identified ERBB1/ERBB2/ERBB4 as CSE1L interactors. Mechanistically, hetero-dimerized ERBB receptors interact with importin-α/β complexes and re-localize to the nucleus, corroborating previous observations of receptors’ nuclear translocation. Intriguingly, we observed that Doxycycline-induced knockdown of clathrin heavy chain (CLTC, involved in intracellular trafficking of receptors via endocytosis) synergizes with ERBB activation to increase the DE-phenotype penetrance. Using ChIP-Seq, we found that ERBB1 binds to the locus of microRNA, miR205, which negatively regulates the expression of importin-α, mainly KPNA1. These results indicate that ERBB receptors translocated to the nucleus reduce the DE-phenotype by inhibiting importins via miR205, while CSE1L induction relieves this inhibition by reducing the receptor's nuclear accumulation. Taken together, these results show that nucleocytoplasmic shuttling of receptors in ERBB-active breast epithelia generates tunable cross-inhibitory feedback through nucleocytoplasmic transport that results in long-term, heterogeneous multicellular fates. Citation Format: Lixin Wang, Bishal Paudel, Anthony McKnight, Kevin Janes. Divergentnucleocytoplasmic transport influences escape from HER2-activated DCIS-like state [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2565.
Abstract 6012: Comparison of pre-analytical methods for DNA methylation analysis of cfDNA
Authors: Miljana Tanic, Oluwadunni Emiloju, Pawan Dhami, Stephan Beck
Journal: Cancer Research (2023)

Abstract Liquid biopsies in the form of cell-free circulating tumor DNA (ctDNA) isolated from blood plasma or serum have shown great promise to be used as minimally-invasive markers in cancer patients providing an insight into the composition of both primary tumor and metastases, and an opportunity to assess clonal dynamics throughout the course of disease. CtDNA carries not only tumor- specific changes in its sequence but also distinctive epigenetic marks, namely DNA methylation patterns similar to the patterns in the primary tumor. Deregulation of tissue-specific DNA methylation patterns is an early event in carcinogenesis holding great promise to be exploited for early detection of cancer. However, in contrast to mutation detection, targeted DNA methylation sequencing of cfDNA remains a challenge due to low concentration and heavy fragmentation. The limiting step in detection of any analyte is the recovery of the DNA molecules. The pre-analytical steps in the DNA methylation detection pipeline include extraction of cfDNA molecules and their conversion using sodium bisulfite. Bisulfite conversion is a harsh chemical reaction that induces further fragmentation and degradation of already scarce cfDNA. In this study we compared commercial methods for cfDNA extraction and for bisulfite conversion to evaluate the yield, degradation and procedural loss. We compared five commercial kits for cfDNA extraction from blood plasma, three column-based (Qiagen’s QIAamp Circulating nucleic acids kit, Norgen’s Plasma/Serum Cell-Free Circulating DNA Purification and Macherey-Nagel’s NucleoSpin® Plasma XS) and two based on magnetic beads cleanup (Bioo Scientific’s Next Prep magnetic Cell-Free Circulating DNA isolation kitand Applied Biosystems’ Magmax Cell-Free Circulating DNA isolation kit. The kits used for bisulfite conversion were Zymo EZ DNA Methylation Lightning with column based purification and with magnetic beads purification, Zymo EZ DNA Methylation Direct with column based purification and with magnetic bead purification, Qiagen Epitect Fast DNA Bisulfite and Diagenode Premium Bisulfite kits. Same samples were processed by each of the kits, Sample degradation was determined using Agilent Bioanalyzer dsDNA kit. Yield was evaluated by Picogreen, absolute qPCR for single-copy gene and for contamination of gDNA by a B-cell specific assay, while procedural loss was determined based on the recovery of a synthetic spike-in. Citation Format: Miljana Tanic, Oluwadunni Emiloju, Pawan Dhami, Stephan Beck. Comparison of pre-analytical methods for DNA methylation analysis of cfDNA. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6012.
Abstract 4089: PanCAR-specific antibody-cytokine fusion proteins
Authors: John T. Keane, Avery D. Posey
Journal: Cancer Research (2023)

Abstract CAR-T cells are a potent immunotherapy that redirect T cell specificity towards cell surface tumor-associated antigens. While this therapy has been effective in hematological malignancies, therapies against solid tumors not achieved the same efficacy due to a multitude of additional challenges, including a lack of tumor specific antigens and an immunosuppressive tumor microenvironment. One strategy to increase T cell potency is to use fourth generation CAR-T cells that also secrete an immunostimulatory factor, such as a cytokine. We have created CAR-T cells targeting Tn-MUC1 utilizing a scFv from the 5E5 antibody that also secrete interleukin-12 (IL-12), interleukin-18 (IL-18), and interleukin-23 (IL-23). These cytokine-secreting CAR-T cells have shown an increase in efficacy against multiple epithelial based tumors in impedance-based killing assays. In a xenograft model of human breast cancer, CAR-T cells secreting IL-12 and IL-23 were able to significantly delay tumor growth compared to non-transduced T cells, CAR-T cells alone, and CAR-T cells secreting IL-18. While these cells showed good efficacy in vivo, clinical translation is difficult due to concerns over cytokine storm due to the constitutive secretion of cytokines. To overcome this, we created a fusion protein utilizing an antibody specific to an invariant region found in majority of CAR molecules, including those utilized commercially available therapies and under pre-clinical development, fused to the three immunostimulatory cytokines. In impedance-based killing assays, antibody-cytokine fusions stimulated non-cytokine secreting CAR-T cells to completely clear the tumor at an E:T ratio in which the CAR-T cells incubated with only the antibody alone were unable to control the tumor growth. Interestingly, combination therapy of CAR-T cells and antibody-cytokine fusions outperformed CAR-T cells constitutively secreting the same cytokines in in vitro assays. This work highlights the use of a single reagent capable of increasing the efficacy of the majority of CAR-T cell therapies and may be an important contribution towards treating solid tumor malignancies with CAR-T cell therapies. Citation Format: John T. Keane, Avery D. Posey. PanCAR-specific antibody-cytokine fusion proteins. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4089.
Abstract 4148: Immunophenotyping of responses to immunotherapy in syngeneic tumor models using multiplex immunofluorescence compared to multiparametric flow cytometry
Authors: Philipp Metzger, Carla Castro, Cynthia Obodozie, Holger Weber
Journal: Cancer Research (2023)

Abstract In the last decades, several major breakthroughs in cancer treatment were achieved through a better understanding and therapeutic targeting of the immune system. Multiparametric flow cytometry is a robust and powerful tool to evaluate the frequency and activation status of a large variety of immune cells. However, for flow cytometric analysis tumor, tissue must be digested into a single cell suspension, and thereby the information on the tumor architecture as well as the spatial distribution of immune cells is lost. The distribution of immune cells in the tumor microenvironment is often heterogeneous and a favorable immune cell distribution is crucial for an efficacious anti-tumor immunotherapy. The recent advances in multiplex immunofluorescence (mIF) allows the analysis of multiple parameters simultaneously so that the frequency as well as the spatial distribution of multiple immune cells can be analyzed. In this study, immunotherapy-responsive tumor cell lines (colon carcinoma cell lines MC38-CEA and CT26wt as well as melanoma cell line Clone M3) were implanted in the mammary fat pad (subQperiorTM), which leads to reduce ulceration rate and homogenous tumor growth compared to subcutaneous implantation. Anti-PD-1 immunotherapy reduced the tumor growth in all three tumor models significantly. Formalin-fixed paraffin-embedded tumor samples were collected from control and anti-PD-1 treated animals. Murine specific InSituPlex® (ISP) technology (Ultivue) was used to perform multiplex immune profiling of the markers CD3, CD4, CD8 and FOXP3 on mouse whole slide FFPE tumor serial sections. Slides were then imaged for high quality images of the four targets and downstream analysis performed. The evaluated T cell frequency and spatial distribution was compared to flow cytometric data of anti-PD-1 treatment in these models. In summary, flow cytometry and multiplex immunofluorescence (mIF) are valuable tools in the evaluation of immune responses in pre-clinical tumor models. Both technologies enable an improved understanding of treatment responses and facilitate the development of novel treatment modalities as well as the identification of potential predictive biomarkers. Citation Format: Philipp Metzger, Carla Castro, Cynthia Obodozie, Holger Weber. Immunophenotyping of responses to immunotherapy in syngeneic tumor models using multiplex immunofluorescence compared to multiparametric flow cytometry. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4148.
Abstract 4751: The function of bromodomain containing protein 4 (BRD44) in hematopoiesis
Authors: Francine Nihozeko
Journal: Cancer Research (2023)

Abstract Bromodomain containing protein 4 (BRD4) is an epigenetic transcription regulator that reads acetylated chromatin and is involved in the recruitment of transcriptional factors to initiate gene transcription. BRD4 is functionally versatile and has extensively been studied for its role in cell cycle progression, gene transcription regulation, chromatin organization and remodeling, as well as DNA replication and repair. In addition, BRD4 has been implicated in many solid and liquid tumors, and its inhibition shows promising preclinical activity, especially in hematopoietic malignancies. BRD4 is overexpressed in Leukemia and has been reported to play a role in hematopoietic stem cell expansion and progenitor development. However, the mechanisms of BRD4 in hematopoietic stem cell functions and disease development remain poorly understood. Using BRD44 knockout (BRD44 Δ/Δ, driven by Mx1 Cre to delete BRD44 in hematopoietic system) mouse model, we found that BRD4 is required for HSCs self-renewal and the loss of BRD44 impaired erythroid differentiation and skewed myeloid differentiation. BRD44 Δ/Δ HSPCs showed G0/G1 arrest, decreased S-phase, and increased senescence compared to wild type (WT) HSPCs. Our study demonstrates that BRD4 is essential for normal hematopoiesis. To further investigate the role of BRD4 in hematopoiesis, we generated BRD44 transgenic mice (driven by Vav1 promoter, to assure all BRD44 transgene expression is instructed in the hematopoietic system). Ongoing studies focus on determining the impact of BRD4 overexpression on hematopoietic stem cell functions. Citation Format: Francine Nihozeko. The function of bromodomain containing protein 4 (BRD44) in hematopoiesis. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4751.
Abstract 5112: Immune biomarkers of clinical response after NSAID treatment in combination with vaccination targeting EGFR-COX2-CDC25B in the APC(Min/+) mouse model
Authors: Denise L. Cecil, Ying Liu, Lauren Corulli, Mary L. Disis
Journal: Cancer Research (2023)

Abstract Studies from our group have shown that administration of NSAIDs in mouse models of Familial Adenomatous Polyposis (FAP) results in a decrease in the development in small intestinal polyps with a significant increase in CD8 tumor infiltrating lymphocytes (TIL) and downregulation of PD-L1 on tumors. Furthermore, we have demonstrated that NSAIDs could be used in combination with vaccination to even further reduce the development of intestinal polyps. We questioned what tissue specific biomarkers could define the efficacy of response with the combination treatment. APC(Min/+) male and female mice (4-6 weeks old) were immunized with a multi-antigen (EGFR, COX2, CDC25B) peptide vaccine with CFA/IFA as an adjuvant. Control mice received immune adjuvant alone. Regular chow or chow containing 400 ppm naproxen was provided intermittently (3 weeks on, 3 weeks off for 3 cycles) or continuously (18 weeks on) at the initiation of the vaccine regimen. Animals were euthanized at 22 weeks and tumors quantified. TIL were evaluated by flow cytometry. Since intermittent naproxen treatment was just as effective at inhibiting tumor development as continuous naproxen treatment, with or without vaccine, we did not differentiate between NSAID regimens. We observed an increase in CD8+ (83%; p&amp;lt;0.0001), Tbet+CD4+ (94%; p&amp;lt;0.001), effector memory (EM) CD4+ (76%; p&amp;lt;0.0001) and EM CD8+ (94%; p&amp;lt;0.0001) TIL in the tumors that did develop in the mice treated with the combination NSAID and vaccination as compared to control. There was increased CD8+ (Pearson correlation coefficient: −0.506, p&amp;lt;0001), Tbet+CD4+ (Pearson correlation coefficient: -0.6222, p&amp;lt;0.001), EM CD4+ (Pearson correlation coefficient: 0.-6074, p&amp;lt;0.001) and EM CD8+ (Pearson correlation coefficient: -0.7155, p&amp;lt;0.001) in mice with greater tumor inhibition than those with less protection. Receiver operator curves revealed that CD8+ (AUC: 0.7623; p=0.002), Tbet+CD4+ (AUC 0.7273; p=0.008), EM CD4+ (AUC 0.6782; p=0.04) and EM CD8 (AUC 0.7897; p&amp;lt;0.001) TIL can differentiate mice receiving the combination of NSAID and vaccination as compared to either monotherapy alone. These data define potential biomarkers of response that can guide human clinical trials of NSAIDs +/- vaccination in patients with FAP. Citation Format: Denise L. Cecil, Ying Liu, Lauren Corulli, Mary L. Disis. Immune biomarkers of clinical response after NSAID treatment in combination with vaccination targeting EGFR-COX2-CDC25B in the APC(Min/+) mouse model. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5112.